RE: [PyMOL] SQL in function with cmd.extend

Andreas, I don't understand the problem as described, but after cmd.extend("domainDef", domainDef) the following should work from PyMOL's command line: domainDef 25880E, 1tab No, there is not a "pause" in PyMOL, though we could probably use one... Cheers, Warren -- Warren L. DeLano,

RE: [PyMOL] How do I color and label unit cell

Lan, Try color color-name, object-name This action both sets the default object color which is used for the cell as well as coloring all of the atoms. Then you can recolor the atoms independently. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Sc

RE: [PyMOL] split screen with their own repair

Geoui, This is something I definitely plan to implement in PyMOL, but it doesn't exist yet. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 . Biz:(65

RE: [PyMOL] Multiple ATOM selection

Jon, > To group the following atoms: > > ATOM688 CG ASP A 87 > ATOM689 OD1 ASP A 87 > ATOM690 OD2 ASP A 87 > ATOM 1247 OG SER A 157 > ATOM 1259 OG1 THR A 159 > ATOM 1861 CZ3 TRP A 234 > ATOM 1862 CH2 TRP A 234 select mysel, a/87/cg+od1+

RE: [PyMOL] Error opening saved .pse file

Sushmita, This looks like a truncated session file, which happens if PyMOL was quit while it was still writing a session file. Unfortunately, there is no way to recover the contents of that session. In order to avoid this problem in the future, please take care to insure that your session file

Re: [PyMOL] Multiple ATOM selection

select thingy, id 688+689+690+1247+1259+1961+1862 - for some reason, 688-690... doesn't seem to work for me - i've had problems with id in the past .. PyMOL used to re-number things, but i don't think it re-numbers them these days (i could easily be wrong about this) - be careful in scri

[PyMOL] Multiple ATOM selection

Greetings, I want to define and display a patch of functionally related atoms on a protein-- but only the individual atoms of interest, not the entire residues to which they might belong. Is there a way to select atoms by their serial number in the PDB file, rather than name or residue membership

[PyMOL] How do I color and label unit cell

Hello, I would like to display crystal packing of my molecule with unit cell labeled and colored in black. I was able to show the unit cell by using the command, (show cell, hex). But I could not figure out how to change the color of the unit cell, the default color is orange. I also want to lab

[PyMOL] Error opening saved .pse file

Hi, I am trying to open a *.pse file and I keep getting the following error: Error: 1 EOFError Exception in Tk callback Function: > (type: ) Args: () Traceback (innermost last): File "C:\Program Files\DeLano Scientific\PyMOL/modules\Pmw\Pmw_1_2\lib\PmwBase.py", line 1747, in __call__

[PyMOL] split screen with their own repair

Hi everybody, is anyone know how i can split the screen into different windows and load different protein in each window. To be more precise, i have 5 different proteins and i would like to have them all at the same time on the screen, but I would like them to have their own repair, just like i

Re: [PyMOL] combining models in a biounit

not sure, but ... the chain ids are identical for both models. this might cause problems, when you merge both models into the same pdb file. try renaming the chain id of your second molecule... cheers, peter On Friday 28 January 2005 23:00, Michael George Lerner wrote: > hi, > > i want to c

[PyMOL] SQL in function with cmd.extend

Hi all, I want to color code scop domains in PDB entries by querrying a database server. It works fine if I just call the function from the python script, however if I define the function to be a Pymol fct, the call from pymol causes an undefined MySQL Error in subchainString: Traceback (mos